Dear Justin:<br><br>Yes. Before I do the water+polymer, I did both the bulk systems separately. The density of TIP5P I mentioned earlier is the results for pure water bulk system. My concern is that if it is reasonable that the property of the system changes with different mdp conditions? Since when I did the bulk water and bulk polymer system, I found the densities change with different cutoff and vdwtype conditions. Is this a artifact? Or the larger cutoff, the more accurate result we can get?<br>
<br><div class="gmail_quote">On Mon, May 18, 2009 at 4:10 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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<br>
Yanmei Song wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Mark:<br>
<br>
Thanks for your answer. I have to use the same mdp file for both water and another polymer molecules in my system, right? Then if the shift function works well for the polymer, I can not get the best result for TIP5P? The density of TIP5P is different from the literature value of 982. Thanks!<br>
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So your system is water + polymer? In that case, you have an added variable - the interaction between the water and your polymer. What you should probably be more concerned with the what the bulk density of the whole system is. I have found that analyzing densities of portions of mixed systems does not give an accurate result.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
<br>
On Mon, May 18, 2009 at 3:33 PM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>> wrote:<br>
<br>
Yanmei Song wrote:<br>
<br>
Dear All:<br>
<br>
I found when I changed the vdwtype from cut-off to shift, the<br>
density of the system decrease significantly.All the other<br>
setting in the mdp file remain unchanged. For example the<br>
density of TIP5P water drops to 962. Does it mean I can not use<br>
the shift for vdwtype?<br>
<br>
<br>
Maybe not. Check out the paper in which TIP5P was parameterized. The<br>
greater the extent to which your .mdp conditions differ from those<br>
conditions, the greater the likelihood that the parameterization is<br>
no longer valid.<br>
<br>
Mark<br>
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-- <br>
Yanmei Song<br>
Ph.D. Candidate<br>
Department of Chemical Engineering<br>
Arizona State University<br>
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========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Yanmei Song<br>Ph.D. Candidate<br>Department of Chemical Engineering<br>Arizona State University<br>